Malian Prime Minister Cheick Modibo Diarra's resignation after his arrest by soldiers is not a coup and a new premier will be named soon, the spokesman for the country's ex-junta says.

"This is not a new coup d'etat," Bakary Mariko told France 24 television on Tuesday after Diarra's arrest on the orders of Mariko's boss, former coup leader Amadou Sanogo.

Mariko said Diarra was "not a man of duty" and added that a successor will "be named in the coming hours by the president".

Diarra, an astrophysicist who has worked on several NASA space programs and served as Microsoft chairman for Africa, was due to leave for Paris on Monday for a medical check-up.

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The resignation plunges further into chaos a country already effectively split in two after armed Islamists linked to al-Qaeda and Tuareg rebels took control of the vast desert north.

Mariko said Diarra, who backed plans to send in a West African intervention force to drive out the extremists who are running the zone according to their brutal interpretation of sharia law, had not fulfilled his task.

Such foreign intervention is fiercely opposed by Sanogo, who launched a coup on March 22 to oust President Amadou Toumani Toure's government only six weeks before an election marking the end of his time in office.

"He had two main missions - to free the north and to organise free and transparent elections," Mariko said, accusing Diarra of only working to "hold on to power eternally".

"The Malian army has the necessary resources and the will to go and liberate the country," he said.

"If the international community drags its feet, the Malian army will assume its responsibilities to liberate its territory."

European Union foreign ministers on Monday approved plans to deploy an EU military training mission in Mali to help the government regain control of the north.